ClinVar Miner

Submissions for variant NM_014646.2(LPIN2):c.1043C>T (p.Pro348Leu) (rs34676691)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000236377 SCV000292605 likely benign not specified 2016-11-25 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV000020708 SCV000645157 benign Majeed syndrome 2019-12-31 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000859343 SCV001151452 likely benign not provided 2018-11-01 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000020708 SCV001159758 uncertain significance Majeed syndrome 2019-03-27 criteria provided, single submitter clinical testing The LPIN2 c.1043C>T; p.Pro348Leu variant (rs34676691), to our knowledge, is not reported in the medical literature. The variant is described in a GeneReviews as benign, but without sufficient evidence to independently evaluate the pathogenicity (see link below). The variant is listed in the ClinVar database (Variation ID: 21518) and in the general population with an allele frequency of 0.1% (356/282842 alleles including 2 homozygotes) in the Genome Aggregation Database. The amino acid at this position is weakly conserved but computational analyses (SIFT: Damaging, PolyPhen-2: Benign) predict conflicting effects of this variant on protein structure/function. Although there are indications that the variant may be benign, due to limited information, the clinical significance of the variant is uncertain at this time References: Link to Majeed syndrome GeneReviews: https://www.ncbi.nlm.nih.gov/books/NBK1974/
Illumina Clinical Services Laboratory,Illumina RCV000020708 SCV001282579 likely benign Majeed syndrome 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
GeneReviews RCV000020708 SCV000041265 benign Majeed syndrome 2008-09-23 no assertion criteria provided curation Converted during submission to Benign.

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